3.1. rand_wc_model_gen package

3.1.1. Subpackages

• 3.1.1.1. rand_wc_model_gen.analysis package
  • 3.1.1.1.1. Subpackages
    • 3.1.1.1.1.1. rand_wc_model_gen.analysis.kb package
      • 3.1.1.1.1.1.1. Module contents
    • 3.1.1.1.1.2. rand_wc_model_gen.analysis.model package
      • 3.1.1.1.1.2.1. Module contents
    • 3.1.1.1.1.3. rand_wc_model_gen.analysis.sim package
      • 3.1.1.1.1.3.1. Submodules
      • 3.1.1.1.1.3.2. rand_wc_model_gen.analysis.sim.rna module
      • 3.1.1.1.1.3.3. Module contents
  • 3.1.1.1.2. Submodules
  • 3.1.1.1.3. rand_wc_model_gen.analysis.core module
  • 3.1.1.1.4. Module contents
• 3.1.1.2. rand_wc_model_gen.config package
  • 3.1.1.2.1. Submodules
  • 3.1.1.2.2. rand_wc_model_gen.config.core module
  • 3.1.1.2.3. Module contents
• 3.1.1.3. rand_wc_model_gen.kb_gen package
  • 3.1.1.3.1. Submodules
  • 3.1.1.3.2. rand_wc_model_gen.kb_gen.chrs_genes_tus module
  • 3.1.1.3.3. rand_wc_model_gen.kb_gen.compartments module
  • 3.1.1.3.4. rand_wc_model_gen.kb_gen.core module
  • 3.1.1.3.5. rand_wc_model_gen.kb_gen.genome module
  • 3.1.1.3.6. rand_wc_model_gen.kb_gen.metabolites module
  • 3.1.1.3.7. rand_wc_model_gen.kb_gen.observables module
  • 3.1.1.3.8. rand_wc_model_gen.kb_gen.properties module
  • 3.1.1.3.9. rand_wc_model_gen.kb_gen.rna module
  • 3.1.1.3.10. rand_wc_model_gen.kb_gen.test module
  • 3.1.1.3.11. Module contents
• 3.1.1.4. rand_wc_model_gen.model_gen package
  • 3.1.1.4.1. Submodules
  • 3.1.1.4.2. rand_wc_model_gen.model_gen.core module
  • 3.1.1.4.3. Module contents

3.1.2. Submodules

3.1.3. rand_wc_model_gen.__main__ module

Command line programs for generating random whole-cell models

Author

Jonathan Karr <karr@mssm.edu>

Author

Ashwin Srinivasan <ashwins@mit.edu>

Date

2018-05-15

Copyright

2018, Karr Lab

License

MIT

class rand_wc_model_gen.__main__.AnalyzeController(*args, **kw)

Bases: cement.ext.ext_argparse.ArgparseController

Analyze a random whole-cell knowledge base, model, and their simulations

class Meta

Bases: object

arguments = [(['--config-path'], {'type': <class 'str'>, 'default': None, 'help': 'Path to configuration file'})]

description = 'Analyze a random whole-cell model and simulations'

help = 'Analyze a random whole-cell model and simulations'

label = 'analyze'

stacked_on = 'base'

stacked_type = 'nested'

class rand_wc_model_gen.__main__.App(label=None, **kw)

Bases: cement.core.foundation.App

Command line application

results

handler results

Type

object

class Meta

Bases: object

base_controller = 'base'

handlers = [<class 'rand_wc_model_gen.__main__.BaseController'>, <class 'rand_wc_model_gen.__main__.GenerateController'>, <class 'rand_wc_model_gen.__main__.SimulateController'>, <class 'rand_wc_model_gen.__main__.AnalyzeController'>]

label = 'rand-wc-model-gen'

class rand_wc_model_gen.__main__.BaseController(*args, **kw)

Bases: cement.ext.ext_argparse.ArgparseController

Base controller for command line application

class Meta

Bases: object

arguments = [(['-v', '--version'], {'action': 'version', 'version': '0.0.1'})]

description = 'Random whole-cell model generator'

help = 'Random whole-cell model generator'

label = 'base'

class rand_wc_model_gen.__main__.GenerateController(*args, **kw)

Bases: cement.ext.ext_argparse.ArgparseController

Generate a random whole-cell knowledge base and a random whole-cell model

class Meta

Bases: object

arguments = [(['--config-path'], {'type': <class 'str'>, 'default': None, 'help': 'Path to configuration file'})]

description = 'Generate a random whole-cell knowledge base and a random whole-cell model'

help = 'Generate a random whole-cell knowledge base and a random whole-cell model'

label = 'generate'

stacked_on = 'base'

stacked_type = 'nested'

class rand_wc_model_gen.__main__.SimulateController(*args, **kw)

Bases: cement.ext.ext_argparse.ArgparseController

Simulate a random whole-cell model

class Meta

Bases: object

arguments = [(['--config-path'], {'type': <class 'str'>, 'default': None, 'help': 'Path to configuration file'}), (['--seed'], {'type': <class 'int'>, 'default': None, 'help': 'Random number generator seed'})]

description = 'Simulate a random whole-cell model'

help = 'Simulate a random whole-cell model'

label = 'simulate'

stacked_on = 'base'

stacked_type = 'nested'

rand_wc_model_gen.__main__.main()

3.1.4. rand_wc_model_gen._version module

3.1.5. Module contents